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Conserved domains on  [gi|880940643|ref|WP_048684843|]
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MULTISPECIES: Rpn family recombination-promoting nuclease/putative transposase [Lactobacillus]

Protein Classification

nuclease/transposase family protein( domain architecture ID 1563233)

PD-(D/E)XK nuclease/transposase family protein similar to the recombination-promoting nuclease RpnA, which is a low activity DNA endonuclease active on single- and double-stranded DNA, but not RNA, with little sequence specificity

EC:  3.1.21.-
PubMed:  28096446

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
T_den_put_tspse super family cl39163
conserved hypothetical protein (putative transposase or invertase); Several lines of evidence ...
 13-272 7.47e-40

conserved hypothetical protein (putative transposase or invertase); Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754.


The actual alignment was detected with superfamily member TIGR01784:

Pssm-ID: 273806 [Multi-domain]  Cd Length: 270  Bit Score: 139.45  E-value: 7.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   13 TDDPVFSWVM--EQDDNCCKLLQAILPEL-NITRVEFETQKRLKFHPEKRGTIPDILAYDQEGRVYDIELQVLQNKFLAQ 89
Cdd:TIGR01784   1 PHDFLFKQLFgdENEDFLIIFLNAVLGELlDIKTLELSSQSFVEENLEDKFSDLDILATDSEGLHYNIEHQVAPDKDMAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   90 RIRYYFSMIDQNLLMSGGKYRDLPETYVIFILPNDPYDQDEKYYEFaFQQLKRKNPLVLDTKQHAIILNASGSIGEVTPR 169
Cdd:TIGR01784  81 RMLYYWSAMYQSQLKQGDKYVVLAPTVFINILPFDLFGDEERVHNI-YLSEEEDSIFELTDLQELHLLELPKLKAIIDER 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643  170 LQG----FFDLIHDKISTKDEFIEKLNREVKKFGTD----PGRRKELMDYQMRLDD--EREFGKEQGKQKEQISSIKRLI 239
Cdd:TIGR01784 160 LLDvldrWLLLLKGKDNQSVNLIFLQIPFIQKAEEEiktlLLSSKELELYEQREKYmtDAISAEEEGKEEGIEEGILEAK 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 880940643  240 KMARQFKASDDFILKQLMEDYGdnFSKSELQEL 272
Cdd:TIGR01784 240 LETAKKLLKNGLTLEQVAEATG--LSVEELEEI 270
 
Name Accession Description Interval E-value
T_den_put_tspse TIGR01784
conserved hypothetical protein (putative transposase or invertase); Several lines of evidence ...
 13-272 7.47e-40

conserved hypothetical protein (putative transposase or invertase); Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754.


Pssm-ID: 273806 [Multi-domain]  Cd Length: 270  Bit Score: 139.45  E-value: 7.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   13 TDDPVFSWVM--EQDDNCCKLLQAILPEL-NITRVEFETQKRLKFHPEKRGTIPDILAYDQEGRVYDIELQVLQNKFLAQ 89
Cdd:TIGR01784   1 PHDFLFKQLFgdENEDFLIIFLNAVLGELlDIKTLELSSQSFVEENLEDKFSDLDILATDSEGLHYNIEHQVAPDKDMAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   90 RIRYYFSMIDQNLLMSGGKYRDLPETYVIFILPNDPYDQDEKYYEFaFQQLKRKNPLVLDTKQHAIILNASGSIGEVTPR 169
Cdd:TIGR01784  81 RMLYYWSAMYQSQLKQGDKYVVLAPTVFINILPFDLFGDEERVHNI-YLSEEEDSIFELTDLQELHLLELPKLKAIIDER 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643  170 LQG----FFDLIHDKISTKDEFIEKLNREVKKFGTD----PGRRKELMDYQMRLDD--EREFGKEQGKQKEQISSIKRLI 239
Cdd:TIGR01784 160 LLDvldrWLLLLKGKDNQSVNLIFLQIPFIQKAEEEiktlLLSSKELELYEQREKYmtDAISAEEEGKEEGIEEGILEAK 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 880940643  240 KMARQFKASDDFILKQLMEDYGdnFSKSELQEL 272
Cdd:TIGR01784 240 LETAKKLLKNGLTLEQVAEATG--LSVEELEEI 270
PDDEXK_2 pfam12784
PD-(D/E)XK nuclease family transposase; Members of this family belong to the PD-(D/E)XK ...
 31-133 1.34e-06

PD-(D/E)XK nuclease family transposase; Members of this family belong to the PD-(D/E)XK nuclease superfamily. These proteins are transposase proteins.


Pssm-ID: 432783  Cd Length: 228  Bit Score: 48.04  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   31 LLQAIL--PELNITRVEFETQKRLKFHPEKRGTIPDILAYDQEGRVYDIELQVLQNKFLAQRIRYYFSMIDQNLLMSGGK 108
Cdd:pfam12784  22 FLNAILkgEKGRIADIEYLNNELLKEYEEDKKSILDIKCKTENGEIINIEMQKSWQYNFKERSLYYWSRLYSEQLKKGQE 101

                          90       100
                  ....*....|....*....|....*
gi 880940643  109 YRDLPETYVIFILpNDPYDQDEKYY 133
Cdd:pfam12784 102 YKELKKVYTINIL-DFGFDDDSSKY 125
 
Name Accession Description Interval E-value
T_den_put_tspse TIGR01784
conserved hypothetical protein (putative transposase or invertase); Several lines of evidence ...
 13-272 7.47e-40

conserved hypothetical protein (putative transposase or invertase); Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754.


Pssm-ID: 273806 [Multi-domain]  Cd Length: 270  Bit Score: 139.45  E-value: 7.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   13 TDDPVFSWVM--EQDDNCCKLLQAILPEL-NITRVEFETQKRLKFHPEKRGTIPDILAYDQEGRVYDIELQVLQNKFLAQ 89
Cdd:TIGR01784   1 PHDFLFKQLFgdENEDFLIIFLNAVLGELlDIKTLELSSQSFVEENLEDKFSDLDILATDSEGLHYNIEHQVAPDKDMAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   90 RIRYYFSMIDQNLLMSGGKYRDLPETYVIFILPNDPYDQDEKYYEFaFQQLKRKNPLVLDTKQHAIILNASGSIGEVTPR 169
Cdd:TIGR01784  81 RMLYYWSAMYQSQLKQGDKYVVLAPTVFINILPFDLFGDEERVHNI-YLSEEEDSIFELTDLQELHLLELPKLKAIIDER 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643  170 LQG----FFDLIHDKISTKDEFIEKLNREVKKFGTD----PGRRKELMDYQMRLDD--EREFGKEQGKQKEQISSIKRLI 239
Cdd:TIGR01784 160 LLDvldrWLLLLKGKDNQSVNLIFLQIPFIQKAEEEiktlLLSSKELELYEQREKYmtDAISAEEEGKEEGIEEGILEAK 239

                         250       260       270
                  ....*....|....*....|....*....|...
gi 880940643  240 KMARQFKASDDFILKQLMEDYGdnFSKSELQEL 272
Cdd:TIGR01784 240 LETAKKLLKNGLTLEQVAEATG--LSVEELEEI 270
PDDEXK_2 pfam12784
PD-(D/E)XK nuclease family transposase; Members of this family belong to the PD-(D/E)XK ...
 31-133 1.34e-06

PD-(D/E)XK nuclease family transposase; Members of this family belong to the PD-(D/E)XK nuclease superfamily. These proteins are transposase proteins.


Pssm-ID: 432783  Cd Length: 228  Bit Score: 48.04  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880940643   31 LLQAIL--PELNITRVEFETQKRLKFHPEKRGTIPDILAYDQEGRVYDIELQVLQNKFLAQRIRYYFSMIDQNLLMSGGK 108
Cdd:pfam12784  22 FLNAILkgEKGRIADIEYLNNELLKEYEEDKKSILDIKCKTENGEIINIEMQKSWQYNFKERSLYYWSRLYSEQLKKGQE 101

                          90       100
                  ....*....|....*....|....*
gi 880940643  109 YRDLPETYVIFILpNDPYDQDEKYY 133
Cdd:pfam12784 102 YKELKKVYTINIL-DFGFDDDSSKY 125
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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